Learn English – What words sound like opposites but are synonyms

To did not come from unto (if anything, vice versa), so the situation is not the same as with flammable and inflammable. Though to is an older form, unto was never as prevalent, and is now either archaic, or used in limited contexts, such as shown here (Idiom: unto itself).

How about false enemies?

I originally voted to close because I thought synonym was an adequate generic term here, but Stephen's comment re false friends prompted me to Google language "false enemies". It seems clear that this coinage has occurred to others (here it is in a Wikipedia talk page, for example).

The first other "clear-cut" example I came up with was ravel / unravel, but I've found a couple more since, as have others here - maybe OP's right, we need a word to Know thine enemy!

EDIT: If an out-and-out neologism is acceptable, there's always the crypto- prefix (secret, hidden, or concealed), so they could be cryptosynonyms (though I must admit that one doesn't yet seem to have occurred to anyone else within the scope of Google's indexing routines).